No. 109 Squadron was formed from the Wireless Intelligence Development Unit at Boscombe Down on 11 December 1940. That unit had been engaged in research into radar and radio navigation aids, both German and and British, and No. 109 continued to perform that role until it was dispersed in January 1942. For the next year the squadron was split into three flights - the Wireless Development Flight, the Wireless Reconnaissance Flight and the Wireless investigation Flight.

The squadron reformed as Boscombe Down in April 1942. Its new role was to aid in the development of the Oboe navigation aid, and then when Oboe was ready to introduce it to service. In August 1943 the squadron moved to Wyton, and became part of the No.8 Group, the Pathfinder Force. After years of experimental work, on 20 December 1943 No. 109 Squadron carried out its first bombing mission, while on 31 December 1943 it led the first raid to use Oboe, an attack on Dusseldorf. The squadron remained part of No.8 Group for the rest of the war, leading the main bomber force over Germany.